forked from D-Net/dnet-hadoop
Merge branch 'beta' into UsageCountOnProjectAndDatasource
This commit is contained in:
commit
477a7c416f
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@ -13,6 +13,8 @@ import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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import com.github.sisyphsu.dateparser.DateParserUtils;
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import com.google.common.collect.Lists;
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@ -23,8 +25,6 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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import me.xuender.unidecode.Unidecode;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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public class GraphCleaningFunctions extends CleaningFunctions {
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@ -27,7 +27,8 @@ object SparkCreateBaselineDataFrame {
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def requestBaseLineUpdatePage(maxFile: String): List[(String, String)] = {
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val data = requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/")
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val result = data.linesWithSeparators.map(l =>l.stripLineEnd)
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val result = data.linesWithSeparators
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.map(l => l.stripLineEnd)
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.filter(l => l.startsWith("<a href="))
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.map { l =>
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val end = l.lastIndexOf("\">")
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@ -63,7 +63,9 @@ class BioScholixTest extends AbstractVocabularyTest {
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val records: String = Source
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.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump"))
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.mkString
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val r: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList
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val r: List[Oaf] = records.linesWithSeparators
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.map(l => l.stripLineEnd)
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.toList
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.map(s => mapper.readValue(s, classOf[PMArticle]))
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.map(a => PubMedToOaf.convert(a, vocabularies))
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assertEquals(10, r.size)
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@ -175,7 +177,8 @@ class BioScholixTest extends AbstractVocabularyTest {
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.mkString
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records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
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val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList.flatMap(o => BioDBToOAF.pdbTOOaf(o))
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val result: List[Oaf] =
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records.linesWithSeparators.map(l => l.stripLineEnd).toList.flatMap(o => BioDBToOAF.pdbTOOaf(o))
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assertTrue(result.nonEmpty)
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result.foreach(r => assertNotNull(r))
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@ -196,7 +199,8 @@ class BioScholixTest extends AbstractVocabularyTest {
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.mkString
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records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
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val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList.flatMap(o => BioDBToOAF.uniprotToOAF(o))
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val result: List[Oaf] =
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records.linesWithSeparators.map(l => l.stripLineEnd).toList.flatMap(o => BioDBToOAF.uniprotToOAF(o))
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assertTrue(result.nonEmpty)
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result.foreach(r => assertNotNull(r))
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@ -241,7 +245,8 @@ class BioScholixTest extends AbstractVocabularyTest {
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.mkString
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records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
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val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).map(s => BioDBToOAF.crossrefLinksToOaf(s)).toList
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val result: List[Oaf] =
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records.linesWithSeparators.map(l => l.stripLineEnd).map(s => BioDBToOAF.crossrefLinksToOaf(s)).toList
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assertNotNull(result)
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assertTrue(result.nonEmpty)
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@ -280,10 +285,13 @@ class BioScholixTest extends AbstractVocabularyTest {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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val l: List[ScholixResolved] = records.linesWithSeparators.map(l =>l.stripLineEnd).map { input =>
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val l: List[ScholixResolved] = records.linesWithSeparators
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.map(l => l.stripLineEnd)
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.map { input =>
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lazy val json = parse(input)
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json.extract[ScholixResolved]
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}.toList
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}
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.toList
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val result: List[Oaf] = l.map(s => BioDBToOAF.scholixResolvedToOAF(s))
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@ -37,12 +37,24 @@ public class SubscriptionUtils {
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}
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public static boolean verifyDateRange(final long date, final String min, final String max) {
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long from = 0;
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long to = Long.MAX_VALUE;
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try {
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return date >= DateUtils.parseDate(min, "yyyy-MM-dd").getTime()
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&& date < DateUtils.parseDate(max, "yyyy-MM-dd").getTime() + ONE_DAY;
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from = min != null ? DateUtils.parseDate(min, "yyyy-MM-dd").getTime() : 0;
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} catch (final ParseException e) {
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return false;
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from = 0;
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}
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try {
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to = max != null ? DateUtils.parseDate(max, "yyyy-MM-dd").getTime() + ONE_DAY : Long.MAX_VALUE;
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} catch (final ParseException e) {
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to = Long.MAX_VALUE;
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}
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return date >= from && date < to;
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}
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public static boolean verifyExact(final String s1, final String s2) {
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@ -41,6 +41,18 @@ public class SubscriptionUtilsTest {
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assertTrue(SubscriptionUtils.verifyDateRange(date, "2010-01-01", "2011-01-01"));
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assertFalse(SubscriptionUtils.verifyDateRange(date, "2020-01-01", "2021-01-01"));
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assertTrue(SubscriptionUtils.verifyDateRange(date, "2010-01-01", "NULL"));
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assertTrue(SubscriptionUtils.verifyDateRange(date, "2010-01-01", null));
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assertTrue(SubscriptionUtils.verifyDateRange(date, "NULL", "2011-01-01"));
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assertTrue(SubscriptionUtils.verifyDateRange(date, null, "2011-01-01"));
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assertTrue(SubscriptionUtils.verifyDateRange(date, "NULL", "NULL"));
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assertTrue(SubscriptionUtils.verifyDateRange(date, null, null));
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assertFalse(SubscriptionUtils.verifyDateRange(date, "2020-01-01", null));
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assertFalse(SubscriptionUtils.verifyDateRange(date, "2020-01-01", "NULL"));
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assertFalse(SubscriptionUtils.verifyDateRange(date, null, "2005-01-01"));
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assertFalse(SubscriptionUtils.verifyDateRange(date, "NULL", "2005-01-01"));
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}
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@Test
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@ -370,10 +370,50 @@ case object Crossref2Oaf {
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case dataset: Dataset => convertDataset(dataset)
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}
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val doisReference: List[String] = for {
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JObject(reference_json) <- json \ "reference"
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JField("DOI", JString(doi_json)) <- reference_json
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} yield doi_json
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if (doisReference != null && doisReference.nonEmpty) {
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val citation_relations: List[Relation] = generateCitationRelations(doisReference, result)
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resultList = resultList ::: citation_relations
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}
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resultList = resultList ::: List(result)
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resultList
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}
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private def createCiteRelation(source: Result, targetPid: String, targetPidType: String): List[Relation] = {
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val targetId = IdentifierFactory.idFromPid("50", targetPidType, targetPid, true)
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val from = new Relation
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from.setSource(source.getId)
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from.setTarget(targetId)
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from.setRelType(ModelConstants.RESULT_RESULT)
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from.setRelClass(ModelConstants.CITES)
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from.setSubRelType(ModelConstants.CITATION)
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from.setCollectedfrom(source.getCollectedfrom)
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from.setDataInfo(source.getDataInfo)
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from.setLastupdatetimestamp(source.getLastupdatetimestamp)
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val to = new Relation
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to.setTarget(source.getId)
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to.setSource(targetId)
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to.setRelType(ModelConstants.RESULT_RESULT)
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to.setRelClass(ModelConstants.IS_CITED_BY)
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to.setSubRelType(ModelConstants.CITATION)
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to.setCollectedfrom(source.getCollectedfrom)
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to.setDataInfo(source.getDataInfo)
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to.setLastupdatetimestamp(source.getLastupdatetimestamp)
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List(from, to)
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}
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def generateCitationRelations(dois: List[String], result: Result): List[Relation] = {
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dois.flatMap(d => createCiteRelation(result, d, "doi"))
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}
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def mappingFunderToRelations(
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funders: List[mappingFunder],
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sourceId: String,
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@ -446,6 +486,7 @@ case object Crossref2Oaf {
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case "10.13039/501100000781" =>
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generateSimpleRelationFromAward(funder, "corda_______", extractECAward)
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generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward)
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generateSimpleRelationFromAward(funder, "corda_____he", extractECAward)
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case "10.13039/100000001" => generateSimpleRelationFromAward(funder, "nsf_________", a => a)
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case "10.13039/501100001665" => generateSimpleRelationFromAward(funder, "anr_________", a => a)
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case "10.13039/501100002341" => generateSimpleRelationFromAward(funder, "aka_________", a => a)
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@ -487,6 +528,34 @@ case object Crossref2Oaf {
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val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63")
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queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
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queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
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//ASAP
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case "10.13039/100018231" => generateSimpleRelationFromAward(funder, "asap________", a => a)
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//CHIST-ERA
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case "10.13039/501100001942" =>
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val targetId = getProjectId("chistera____", "1e5e62235d094afd01cd56e65112fc63")
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queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
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queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
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//HE
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case "10.13039/100018693" | "10.13039/100018694" | "10.13039/100019188" | "10.13039/100019180" |
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"10.13039/100018695" | "10.13039/100019185" | "10.13039/100019186" | "10.13039/100019187" =>
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generateSimpleRelationFromAward(funder, "corda_____he", extractECAward)
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//FCT
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case "10.13039/501100001871" =>
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generateSimpleRelationFromAward(funder, "fct_________", extractECAward)
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//NHMRC
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case "10.13039/501100000925" =>
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generateSimpleRelationFromAward(funder, "mhmrc_______", extractECAward)
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//NIH
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case "10.13039/100000002" =>
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generateSimpleRelationFromAward(funder, "nih_________", extractECAward)
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//NWO
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case "10.13039/501100003246" =>
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generateSimpleRelationFromAward(funder, "nwo_________", extractECAward)
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//UKRI
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case "10.13039/100014013" | "10.13039/501100000267" | "10.13039/501100000268" | "10.13039/501100000269" |
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"10.13039/501100000266" | "10.13039/501100006041" | "10.13039/501100000265" | "10.13039/501100000270" |
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"10.13039/501100013589" | "10.13039/501100000271" =>
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generateSimpleRelationFromAward(funder, "nwo_________", extractECAward)
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case _ => logger.debug("no match for " + funder.DOI.get)
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|
|
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@ -94,7 +94,6 @@
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"family": "Stein",
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"sequence": "first",
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"affiliation": [
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]
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},
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{
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|
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@ -104,7 +103,6 @@
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"family": "Velzen",
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"sequence": "additional",
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"affiliation": [
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|
||||
]
|
||||
},
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{
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|
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@ -114,7 +112,6 @@
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"family": "Kowalski",
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"sequence": "additional",
|
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"affiliation": [
|
||||
|
||||
]
|
||||
},
|
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{
|
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|
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@ -122,7 +119,6 @@
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"family": "Franckowiak",
|
||||
"sequence": "additional",
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"affiliation": [
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|
||||
]
|
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},
|
||||
{
|
||||
|
|
@ -132,7 +128,6 @@
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|||
"family": "Gezari",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -142,7 +137,6 @@
|
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"family": "Miller-Jones",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -150,7 +144,6 @@
|
|||
"family": "Frederick",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -160,7 +153,6 @@
|
|||
"family": "Sfaradi",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -168,7 +160,6 @@
|
|||
"family": "Bietenholz",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -178,7 +169,6 @@
|
|||
"family": "Horesh",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -186,7 +176,6 @@
|
|||
"family": "Fender",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -196,7 +185,6 @@
|
|||
"family": "Garrappa",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -206,7 +194,6 @@
|
|||
"family": "Ahumada",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -214,7 +201,6 @@
|
|||
"family": "Andreoni",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -222,7 +208,6 @@
|
|||
"family": "Belicki",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -232,7 +217,6 @@
|
|||
"family": "Bellm",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -240,7 +224,6 @@
|
|||
"family": "Böttcher",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -248,7 +231,6 @@
|
|||
"family": "Brinnel",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -256,7 +238,6 @@
|
|||
"family": "Burruss",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -266,7 +247,6 @@
|
|||
"family": "Cenko",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -276,7 +256,6 @@
|
|||
"family": "Coughlin",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -286,7 +265,6 @@
|
|||
"family": "Cunningham",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -294,7 +272,6 @@
|
|||
"family": "Drake",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -302,7 +279,6 @@
|
|||
"family": "Farrar",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -310,7 +286,6 @@
|
|||
"family": "Feeney",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -318,7 +293,6 @@
|
|||
"family": "Foley",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -328,7 +302,6 @@
|
|||
"family": "Gal-Yam",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -336,7 +309,6 @@
|
|||
"family": "Golkhou",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -346,7 +318,6 @@
|
|||
"family": "Goobar",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -356,7 +327,6 @@
|
|||
"family": "Graham",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -364,7 +334,6 @@
|
|||
"family": "Hammerstein",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -374,7 +343,6 @@
|
|||
"family": "Helou",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -384,7 +352,6 @@
|
|||
"family": "Hung",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -392,7 +359,6 @@
|
|||
"family": "Kasliwal",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -402,7 +368,6 @@
|
|||
"family": "Kilpatrick",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -412,7 +377,6 @@
|
|||
"family": "Kong",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -422,7 +386,6 @@
|
|||
"family": "Kupfer",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -432,7 +395,6 @@
|
|||
"family": "Laher",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -442,7 +404,6 @@
|
|||
"family": "Mahabal",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -452,7 +413,6 @@
|
|||
"family": "Masci",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -462,7 +422,6 @@
|
|||
"family": "Necker",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -472,7 +431,6 @@
|
|||
"family": "Nordin",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -480,7 +438,6 @@
|
|||
"family": "Perley",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -490,7 +447,6 @@
|
|||
"family": "Rigault",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -500,7 +456,6 @@
|
|||
"family": "Reusch",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -508,7 +463,6 @@
|
|||
"family": "Rodriguez",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -518,7 +472,6 @@
|
|||
"family": "Rojas-Bravo",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -528,7 +481,6 @@
|
|||
"family": "Rusholme",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -538,7 +490,6 @@
|
|||
"family": "Shupe",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -548,7 +499,6 @@
|
|||
"family": "Singer",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -558,7 +508,6 @@
|
|||
"family": "Sollerman",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -566,7 +515,6 @@
|
|||
"family": "Soumagnac",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -574,7 +522,6 @@
|
|||
"family": "Stern",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -582,7 +529,6 @@
|
|||
"family": "Taggart",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -590,7 +536,6 @@
|
|||
"family": "van Santen",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -598,7 +543,6 @@
|
|||
"family": "Ward",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -606,7 +550,6 @@
|
|||
"family": "Woudt",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
},
|
||||
{
|
||||
|
|
@ -616,7 +559,6 @@
|
|||
"family": "Yao",
|
||||
"sequence": "additional",
|
||||
"affiliation": [
|
||||
|
||||
]
|
||||
}
|
||||
],
|
||||
|
|
@ -1412,7 +1354,6 @@
|
|||
"Nature Astronomy"
|
||||
],
|
||||
"original-title": [
|
||||
|
||||
],
|
||||
"language": "en",
|
||||
"link": [
|
||||
|
|
@ -1448,10 +1389,8 @@
|
|||
},
|
||||
"score": 1.0,
|
||||
"subtitle": [
|
||||
|
||||
],
|
||||
"short-title": [
|
||||
|
||||
],
|
||||
"issued": {
|
||||
"date-parts": [
|
||||
|
|
@ -1480,7 +1419,6 @@
|
|||
"URL": "http://dx.doi.org/10.1038/s41550-020-01295-8",
|
||||
"relation": {
|
||||
"cites": [
|
||||
|
||||
]
|
||||
},
|
||||
"ISSN": [
|
||||
|
|
|
|||
|
|
@ -1,9 +1,14 @@
|
|||
package eu.dnetlib.dhp.doiboost.crossref
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf._
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
import eu.dnetlib.doiboost.crossref.Crossref2Oaf
|
||||
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
|
||||
import org.json4s
|
||||
import org.json4s.JsonAST.{JField, JObject, JString}
|
||||
import org.json4s.{DefaultFormats, JValue}
|
||||
import org.json4s.jackson.JsonMethods
|
||||
import org.junit.jupiter.api.Assertions._
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
|
@ -109,6 +114,47 @@ class CrossrefMappingTest {
|
|||
|
||||
}
|
||||
|
||||
private def parseJson(input: String): JValue = {
|
||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||
lazy val json: json4s.JValue = JsonMethods.parse(input)
|
||||
|
||||
json
|
||||
}
|
||||
|
||||
@Test
|
||||
def testCitationRelations(): Unit = {
|
||||
val json = Source
|
||||
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo.json"))
|
||||
.mkString
|
||||
|
||||
assertNotNull(json)
|
||||
assertFalse(json.isEmpty)
|
||||
|
||||
val result: List[Oaf] = Crossref2Oaf.convert(json)
|
||||
|
||||
assertTrue(result.nonEmpty)
|
||||
|
||||
val j = parseJson(json)
|
||||
|
||||
val doisReference: List[String] = for {
|
||||
JObject(reference_json) <- j \ "reference"
|
||||
JField("DOI", JString(doi_json)) <- reference_json
|
||||
} yield doi_json
|
||||
|
||||
val relationList: List[Relation] = result
|
||||
.filter(s => s.isInstanceOf[Relation])
|
||||
.map(r => r.asInstanceOf[Relation])
|
||||
.filter(r => r.getSubRelType.equalsIgnoreCase(ModelConstants.CITATION))
|
||||
|
||||
assertNotNull(relationList)
|
||||
assertFalse(relationList.isEmpty)
|
||||
|
||||
assertEquals(doisReference.size * 2, relationList.size)
|
||||
|
||||
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
|
||||
relationList.foreach(p => println(mapper.writeValueAsString(p)))
|
||||
}
|
||||
|
||||
@Test
|
||||
def testEmptyTitle(): Unit = {
|
||||
val json = Source
|
||||
|
|
|
|||
|
|
@ -25,7 +25,9 @@ class MappingORCIDToOAFTest {
|
|||
.mkString
|
||||
assertNotNull(json)
|
||||
assertFalse(json.isEmpty)
|
||||
json.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => {
|
||||
json.linesWithSeparators
|
||||
.map(l => l.stripLineEnd)
|
||||
.foreach(s => {
|
||||
assertNotNull(ORCIDToOAF.extractValueFromInputString(s))
|
||||
})
|
||||
}
|
||||
|
|
|
|||
|
|
@ -5,7 +5,6 @@ import java.io.IOException;
|
|||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
|
|
@ -27,6 +26,7 @@ import org.slf4j.LoggerFactory;
|
|||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob;
|
||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||
|
||||
public class CleanCountryTest {
|
||||
|
|
@ -185,7 +185,6 @@ public class CleanCountryTest {
|
|||
|
||||
Assertions.assertEquals(0, tmp.first().getCountry().size());
|
||||
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -53,7 +53,8 @@ class ResolveEntitiesTest extends Serializable {
|
|||
def generateUpdates(spark: SparkSession): Unit = {
|
||||
val template = Source.fromInputStream(this.getClass.getResourceAsStream("updates")).mkString
|
||||
|
||||
val pids: List[String] = template.linesWithSeparators.map(l =>l.stripLineEnd)
|
||||
val pids: List[String] = template.linesWithSeparators
|
||||
.map(l => l.stripLineEnd)
|
||||
.map { id =>
|
||||
val r = new Result
|
||||
r.setId(id.toLowerCase.trim)
|
||||
|
|
@ -264,7 +265,8 @@ class ResolveEntitiesTest extends Serializable {
|
|||
Source
|
||||
.fromInputStream(this.getClass.getResourceAsStream(s"publication"))
|
||||
.mkString
|
||||
.linesWithSeparators.map(l =>l.stripLineEnd)
|
||||
.linesWithSeparators
|
||||
.map(l => l.stripLineEnd)
|
||||
.next(),
|
||||
classOf[Publication]
|
||||
)
|
||||
|
|
|
|||
|
|
@ -69,7 +69,8 @@ class ScholixGraphTest extends AbstractVocabularyTest {
|
|||
getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/merge_result_scholix")
|
||||
)
|
||||
.mkString
|
||||
val result: List[(Relation, ScholixSummary)] = inputRelations.linesWithSeparators.map(l =>l.stripLineEnd)
|
||||
val result: List[(Relation, ScholixSummary)] = inputRelations.linesWithSeparators
|
||||
.map(l => l.stripLineEnd)
|
||||
.sliding(2)
|
||||
.map(s => (s.head, s(1)))
|
||||
.map(p => (mapper.readValue(p._1, classOf[Relation]), mapper.readValue(p._2, classOf[ScholixSummary])))
|
||||
|
|
|
|||
|
|
@ -0,0 +1,32 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
|
||||
<parent>
|
||||
<artifactId>dhp-workflows</artifactId>
|
||||
<groupId>eu.dnetlib.dhp</groupId>
|
||||
<version>1.2.4-SNAPSHOT</version>
|
||||
</parent>
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
<artifactId>dhp-monitor-update</artifactId>
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>org.apache.spark</groupId>
|
||||
<artifactId>spark-core_2.11</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.spark</groupId>
|
||||
<artifactId>spark-sql_2.11</artifactId>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
<build>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>pl.project13.maven</groupId>
|
||||
<artifactId>git-commit-id-plugin</artifactId>
|
||||
<version>2.1.11</version>
|
||||
<configuration>
|
||||
<failOnNoGitDirectory>false</failOnNoGitDirectory>
|
||||
</configuration>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
</project>
|
||||
|
|
@ -0,0 +1,34 @@
|
|||
<configuration>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>${jobTracker}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>${nameNode}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.use.system.libpath</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_jdbc_url</name>
|
||||
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1;?spark.executor.memory=19166291558;spark.yarn.executor.memoryOverhead=3225;spark.driver.memory=11596411699;spark.yarn.driver.memoryOverhead=1228</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.wf.workflow.notification.url</name>
|
||||
<value>{serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>stats_tool_api_url</name>
|
||||
<value>${stats_tool_api_url}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -0,0 +1,18 @@
|
|||
export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs
|
||||
export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami)
|
||||
if ! [ -L $link_folder ]
|
||||
then
|
||||
rm -Rf "$link_folder"
|
||||
ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
|
||||
fi
|
||||
|
||||
export SOURCE=$1
|
||||
export TARGET=$2
|
||||
export SCRIPT_PATH=$3
|
||||
|
||||
echo "Getting file from " $3
|
||||
hdfs dfs -copyToLocal $3
|
||||
|
||||
echo "Updating monitor database"
|
||||
cat createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 | impala-shell -f -
|
||||
echo "Impala shell finished"
|
||||
|
|
@ -0,0 +1,146 @@
|
|||
DROP TABLE IF EXISTS TARGET.result_new;
|
||||
|
||||
create table TARGET.result_new as
|
||||
select distinct * from (
|
||||
select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in (
|
||||
-- 'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork
|
||||
-- 'openorgs____::38d7097854736583dde879d12dacafca' -- Brown University
|
||||
'openorgs____::57784c9e047e826fefdb1ef816120d92' --Arts et Métiers ParisTech
|
||||
) )) foo;
|
||||
|
||||
COMPUTE STATS TARGET.result_new;
|
||||
|
||||
INSERT INTO TARGET.result select * from TARGET.result_new;
|
||||
COMPUTE STATS TARGET.result;
|
||||
|
||||
INSERT INTO TARGET.result_citations select * from TARGET.result_citations orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_citations;
|
||||
|
||||
INSERT INTO TARGET.result_references_oc select * from TARGET.result_references_oc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_references_oc;
|
||||
|
||||
INSERT INTO TARGET.result_citations_oc select * from TARGET.result_citations_oc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_citations_oc;
|
||||
|
||||
INSERT INTO TARGET.result_classifications select * from TARGET.result_classifications orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_classifications;
|
||||
|
||||
INSERT INTO TARGET.result_apc select * from TARGET.result_apc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_apc;
|
||||
|
||||
INSERT INTO TARGET.result_concepts select * from TARGET.result_concepts orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_concepts;
|
||||
|
||||
INSERT INTO TARGET.result_datasources select * from TARGET.result_datasources orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_datasources;
|
||||
|
||||
INSERT INTO TARGET.result_fundercount select * from TARGET.result_fundercount orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_fundercount;
|
||||
|
||||
INSERT INTO TARGET.result_gold select * from TARGET.result_gold orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_gold;
|
||||
|
||||
INSERT INTO TARGET.result_greenoa select * from TARGET.result_greenoa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_greenoa;
|
||||
|
||||
INSERT INTO TARGET.result_languages select * from TARGET.result_languages orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_languages;
|
||||
|
||||
INSERT INTO TARGET.result_licenses select * from TARGET.result_licenses orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_licenses;
|
||||
|
||||
INSERT INTO TARGET.result_oids select * from TARGET.result_oids orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_oids;
|
||||
|
||||
INSERT INTO TARGET.result_organization select * from TARGET.result_organization orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_organization;
|
||||
|
||||
INSERT INTO TARGET.result_peerreviewed select * from TARGET.result_peerreviewed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_peerreviewed;
|
||||
|
||||
INSERT INTO TARGET.result_pids select * from TARGET.result_pids orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_pids;
|
||||
|
||||
INSERT INTO TARGET.result_projectcount select * from TARGET.result_projectcount orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_projectcount;
|
||||
|
||||
INSERT INTO TARGET.result_projects select * from TARGET.result_projects orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_projects;
|
||||
|
||||
INSERT INTO TARGET.result_refereed select * from TARGET.result_refereed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_refereed;
|
||||
|
||||
INSERT INTO TARGET.result_sources select * from TARGET.result_sources orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_sources;
|
||||
|
||||
INSERT INTO TARGET.result_topics select * from TARGET.result_topics orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_topics;
|
||||
|
||||
INSERT INTO TARGET.result_fos select * from TARGET.result_fos orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_fos;
|
||||
|
||||
create view TARGET.foo1 as select * from TARGET.result_result rr where rr.source in (select id from TARGET.result_new);
|
||||
create view TARGET.foo2 as select * from TARGET.result_result rr where rr.target in (select id from TARGET.result_new);
|
||||
INSERT INTO TARGET.result_result select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou;
|
||||
drop view TARGET.foo1;
|
||||
drop view TARGET.foo2;
|
||||
COMPUTE STATS TARGET.result_result;
|
||||
|
||||
-- indicators
|
||||
-- Sprint 1 ----
|
||||
INSERT INTO TARGET.indi_pub_green_oa select * from TARGET.indi_pub_green_oa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_green_oa;
|
||||
INSERT INTO TARGET.indi_pub_grey_lit select * from TARGET.indi_pub_grey_lit orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_grey_lit;
|
||||
INSERT INTO TARGET.indi_pub_doi_from_crossref select * from TARGET.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_doi_from_crossref;
|
||||
-- Sprint 2 ----
|
||||
INSERT INTO TARGET.indi_result_has_cc_licence select * from TARGET.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_result_has_cc_licence;
|
||||
INSERT INTO TARGET.indi_result_has_cc_licence_url select * from TARGET.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_result_has_cc_licence_url;
|
||||
INSERT INTO TARGET.indi_pub_has_abstract select * from TARGET.indi_pub_has_abstract orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_has_abstract;
|
||||
INSERT INTO TARGET.indi_result_with_orcid select * from TARGET.indi_result_with_orcid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_result_with_orcid;
|
||||
---- Sprint 3 ----
|
||||
INSERT INTO TARGET.indi_funded_result_with_fundref select * from TARGET.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_funded_result_with_fundref;
|
||||
---- Sprint 4 ----
|
||||
INSERT INTO TARGET.indi_pub_diamond select * from TARGET.indi_pub_diamond orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_diamond;
|
||||
INSERT INTO TARGET.indi_pub_in_transformative select * from TARGET.indi_pub_in_transformative orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_in_transformative;
|
||||
INSERT INTO TARGET.indi_pub_closed_other_open select * from TARGET.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_closed_other_open;
|
||||
---- Sprint 5 ----
|
||||
INSERT INTO TARGET.indi_result_no_of_copies select * from TARGET.indi_result_no_of_copies orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_result_no_of_copies;
|
||||
---- Sprint 6 ----
|
||||
INSERT INTO TARGET.indi_pub_hybrid_oa_with_cc select * from TARGET.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_hybrid_oa_with_cc;
|
||||
INSERT INTO TARGET.indi_pub_downloads select * from TARGET.indi_pub_downloads orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
|
||||
COMPUTE STATS TARGET.indi_pub_downloads;
|
||||
INSERT INTO TARGET.indi_pub_downloads_datasource select * from TARGET.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
|
||||
COMPUTE STATS TARGET.indi_pub_downloads_datasource;
|
||||
INSERT INTO TARGET.indi_pub_downloads_year select * from TARGET.indi_pub_downloads_year orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
|
||||
COMPUTE STATS TARGET.indi_pub_downloads_year;
|
||||
INSERT INTO TARGET.indi_pub_downloads_datasource_year select * from TARGET.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
|
||||
COMPUTE STATS TARGET.indi_pub_downloads_datasource_year;
|
||||
---- Sprint 7 ----
|
||||
INSERT INTO TARGET.indi_pub_gold_oa select * from TARGET.indi_pub_gold_oa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_gold_oa;
|
||||
INSERT INTO TARGET.indi_pub_hybrid select * from TARGET.indi_pub_hybrid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_hybrid;
|
||||
|
||||
INSERT INTO TARGET.indi_pub_has_preprint select * from TARGET.indi_pub_has_preprint orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_has_preprint;
|
||||
INSERT INTO TARGET.indi_pub_in_subscribed select * from TARGET.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_in_subscribed;
|
||||
INSERT INTO TARGET.indi_result_with_pid select * from TARGET.indi_result_with_pid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_result_with_pid;
|
||||
--create table TARGET.indi_datasets_gold_oa stored as parquet as select * from SOURCE.indi_datasets_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--compute stats TARGET.indi_datasets_gold_oa;
|
||||
--create table TARGET.indi_software_gold_oa stored as parquet as select * from SOURCE.indi_software_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--compute stats TARGET.indi_software_gold_oa;
|
||||
DROP TABLE TARGET.result_new;
|
||||
|
|
@ -0,0 +1,77 @@
|
|||
<workflow-app name="Monitor DB" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>stats_db_name</name>
|
||||
<description>the target stats database name</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>stats_db_shadow_name</name>
|
||||
<description>the name of the shadow schema</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>monitor_db_name</name>
|
||||
<description>the target monitor db name</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>monitor_db_shadow_name</name>
|
||||
<description>the name of the shadow monitor db</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>stats_tool_api_url</name>
|
||||
<description>The url of the API of the stats tool. Is used to trigger the cache update.</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
<description>hive server metastore URIs</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_jdbc_url</name>
|
||||
<description>hive server jdbc url</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_timeout</name>
|
||||
<description>the time period, in seconds, after which Hive fails a transaction if a Hive client has not sent a hearbeat. The default value is 300 seconds.</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>context_api_url</name>
|
||||
<description>the base url of the context api (https://services.openaire.eu/openaire)</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>hive.metastore.uris</name>
|
||||
<value>${hive_metastore_uris}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive.txn.timeout</name>
|
||||
<value>${hive_timeout}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="Step1-createMonitorDB"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="Step1-createMonitorDB">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>monitor.sh</exec>
|
||||
<argument>${stats_db_name}</argument>
|
||||
<argument>${monitor_db_name}</argument>
|
||||
<argument>${wf:appPath()}/scripts/createMonitorDB.sql</argument>
|
||||
<file>monitor.sh</file>
|
||||
</shell>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -30,11 +30,16 @@ from rcount
|
|||
group by rcount.pid;
|
||||
|
||||
create view ${stats_db_name}.rndexpenditure as select * from stats_ext.rndexpediture;
|
||||
create view ${stats_db_name}.rndgdpexpenditure as select * from stats_ext.rndgdpexpenditure;
|
||||
create view ${stats_db_name}.doctoratestudents as select * from stats_ext.doctoratestudents;
|
||||
create view ${stats_db_name}.totalresearchers as select * from stats_ext.totalresearchers;
|
||||
create view ${stats_db_name}.totalresearchersft as select * from stats_ext.totalresearchersft;
|
||||
create view ${stats_db_name}.hrrst as select * from stats_ext.hrrst;
|
||||
|
||||
create table ${stats_db_name}.result_instance stored as parquet as
|
||||
select distinct r.*
|
||||
from (
|
||||
select substr(r.id, 4) as id, inst.accessright.classname as accessright, substr(inst.collectedfrom.key, 4) as collectedfrom,
|
||||
select substr(r.id, 4) as id, inst.accessright.classname as accessright, inst.accessright.openaccessroute as accessright_uw, substr(inst.collectedfrom.key, 4) as collectedfrom,
|
||||
substr(inst.hostedby.key, 4) as hostedby, inst.dateofacceptance.value as dateofacceptance, inst.license.value as license, p.qualifier.classname as pidtype, p.value as pid
|
||||
from ${openaire_db_name}.result r lateral view explode(r.instance) instances as inst lateral view explode(inst.pid) pids as p) r
|
||||
join ${stats_db_name}.result res on res.id=r.id;
|
||||
|
|
|
|||
|
|
@ -10,6 +10,11 @@ create view if not exists TARGET.creation_date as select * from SOURCE.creation_
|
|||
create view if not exists TARGET.funder as select * from SOURCE.funder;
|
||||
create view if not exists TARGET.fundref as select * from SOURCE.fundref;
|
||||
create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture;
|
||||
create view if not exists TARGET.rndgdpexpenditure as select * from SOURCE.rndgdpexpenditure;
|
||||
create view if not exists TARGET.doctoratestudents as select * from SOURCE.doctoratestudents;
|
||||
create view if not exists TARGET.totalresearchers as select * from SOURCE.totalresearchers;
|
||||
create view if not exists TARGET.totalresearchersft as select * from SOURCE.totalresearchersft;
|
||||
create view if not exists TARGET.hrrst as select * from SOURCE.hrrst;
|
||||
|
||||
create table TARGET.result stored as parquet as
|
||||
select distinct * from (
|
||||
|
|
@ -50,7 +55,15 @@ create table TARGET.result stored as parquet as
|
|||
'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech
|
||||
'openorgs____::e15adb13c4dadd49de4d35c39b5da93a', -- Nanyang Technological University
|
||||
'openorgs____::4b34103bde246228fcd837f5f1bf4212', -- Autonomous University of Barcelona
|
||||
'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb' -- McMaster University
|
||||
'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb', -- McMaster University
|
||||
'openorgs____::51c7fc556e46381734a25a6fbc3fd398', -- University of Modena and Reggio Emilia
|
||||
'openorgs____::235d7f9ad18ecd7e6dc62ea4990cb9db', -- Bilkent University
|
||||
'openorgs____::31f2fa9e05b49d4cf40a19c3fed8eb06', -- Saints Cyril and Methodius University of Skopje
|
||||
'openorgs____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan
|
||||
'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork
|
||||
'openorgs____::38d7097854736583dde879d12dacafca', -- Brown University
|
||||
'openorgs____::57784c9e047e826fefdb1ef816120d92', --Arts et Métiers ParisTech
|
||||
'openorgs____::2530baca8a15936ba2e3297f2bce2e7e' -- University of Cape Town
|
||||
))) foo;
|
||||
compute stats TARGET.result;
|
||||
|
||||
|
|
|
|||
|
|
@ -70,7 +70,40 @@
|
|||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="Step1"/>
|
||||
<start to="resume_from"/>
|
||||
|
||||
<decision name="resume_from">
|
||||
<switch>
|
||||
<case to="Step1">${wf:conf('resumeFrom') eq 'Step1'}</case>
|
||||
<case to="Step2">${wf:conf('resumeFrom') eq 'Step2'}</case>
|
||||
<case to="Step3">${wf:conf('resumeFrom') eq 'Step3'}</case>
|
||||
<case to="Step4">${wf:conf('resumeFrom') eq 'Step4'}</case>
|
||||
<case to="Step5">${wf:conf('resumeFrom') eq 'Step5'}</case>
|
||||
<case to="Step6">${wf:conf('resumeFrom') eq 'Step6'}</case>
|
||||
<case to="Step7">${wf:conf('resumeFrom') eq 'Step7'}</case>
|
||||
<case to="Step8">${wf:conf('resumeFrom') eq 'Step8'}</case>
|
||||
<case to="Step9">${wf:conf('resumeFrom') eq 'Step9'}</case>
|
||||
<case to="Step10">${wf:conf('resumeFrom') eq 'Step10'}</case>
|
||||
<case to="Step11">${wf:conf('resumeFrom') eq 'Step11'}</case>
|
||||
<case to="Step12">${wf:conf('resumeFrom') eq 'Step12'}</case>
|
||||
<case to="Step13">${wf:conf('resumeFrom') eq 'Step13'}</case>
|
||||
<case to="Step14">${wf:conf('resumeFrom') eq 'Step14'}</case>
|
||||
<case to="Step15">${wf:conf('resumeFrom') eq 'Step15'}</case>
|
||||
<case to="Step15_5">${wf:conf('resumeFrom') eq 'Step15_5'}</case>
|
||||
<case to="Contexts">${wf:conf('resumeFrom') eq 'Contexts'}</case>
|
||||
<case to="Step16-createIndicatorsTables">${wf:conf('resumeFrom') eq 'Step16-createIndicatorsTables'}</case>
|
||||
<case to="Step16_1-definitions">${wf:conf('resumeFrom') eq 'Step16_1-definitions'}</case>
|
||||
<case to="Step16_5">${wf:conf('resumeFrom') eq 'Step16_5'}</case>
|
||||
<case to="Step19-finalize">${wf:conf('resumeFrom') eq 'Step19-finalize'}</case>
|
||||
<case to="step20-createMonitorDB">${wf:conf('resumeFrom') eq 'step20-createMonitorDB'}</case>
|
||||
<case to="step21-createObservatoryDB-pre">${wf:conf('resumeFrom') eq 'step21-createObservatoryDB-pre'}</case>
|
||||
<case to="step21-createObservatoryDB">${wf:conf('resumeFrom') eq 'step21-createObservatoryDB'}</case>
|
||||
<case to="step21-createObservatoryDB-post">${wf:conf('resumeFrom') eq 'step21-createObservatoryDB-post'}</case>
|
||||
<case to="Step22">${wf:conf('resumeFrom') eq 'Step22'}</case>
|
||||
<default to="Step1"/>
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
|
|
|
|||
Loading…
Reference in New Issue